Tuesday, February 2, 2016

Sunday, January 31, 2016

Botany picture #222: Astroloma humifusum


I did not even know we had this species on Mt. Majura until we went for a little walk earlier today: Astroloma humifusum (Ericaceae). Pretty as it is, the leaves are rather unpleasantly prickly. At the recent ASBS conference I learned that phylogenetically, Astroloma are merely colourful Leucopogon. Looking at the leaves and the hairy corolla orifice I can see the affinity.

Have updated the Flora of Mount Majura Nature Reserve post with this and another species I photographed today.

Thursday, January 28, 2016

Aubert's analysis of phylogenetic terminology, final part 8: two parallel classifications

Continuing the discussion of this paper from here, here, here, here, here, here, and here, and working through the main claims of the paper as I see them:
  • The various definitions provided in the paper are in some way better than the ones that are currently accepted.
  • There is no relevant difference between the systematics-relevant relationships and structures existing at any level of the diversity of life. (E.g. mother > daughter is completely equivalent to bony fish > land animals - they can all be drawn as diamonds and arrows, right?)
  • A strictly phylogenetic classification is formally impossible.
  • Cladism is part of structuralism and therefore characterised by "anti-realism and a metaphysical way of thinking".
  • It would be preferable to have two parallel classifications, one of clades and one that includes taxa that are allowed to be non-monophyletic.

Why not have parallel phylogenetic and 'evolutionary' classifications?

Damien Aubert ends his paper with the suggestion to have two parallel classifications: The official system of living organisms should allow paraphyletic taxa, and all the mainstream systematists who want to make groups monophyletic should go away and build up a new, separate system of nested clades.

At this moment one might wonder how this suggestion can be consistent with earlier arguments that (a) a strictly cladistic classification is formally impossible and (b) clades can't be taxa, that is named groups of organisms, anyway. If Aubert believes his own arguments, the separate phylogenetic classification he suggests is not possible. If he believes his solution to be possible, those other arguments must be wrong. Presumably the idea would be that the cladistic system should not be called a classification, and that named groups of organisms are not necessarily taxa, but only if they are paraphyletic. Which doesn't make sense to me because even 'evolutionary' taxonomists have to recognise some monophyletic taxa.

Anyway, let's assume that a phylogenetic classification is possible, and let's also disregard for the moment that Aubert would like to reserve the official, widely used classification for what is currently a non-mainstream, minority position. Why not have two parallel classifications?

Friday, January 22, 2016

Aubert's analysis of phylogenetic terminology, part 7: objective delimitation of paraphyletic groups

Continuing the discussion of this paper from here, here, here, here, here, and here, and working through the main claims of the paper as I see them:
  • The various definitions provided in the paper are in some way better than the ones that are currently accepted.
  • There is no relevant difference between the systematics-relevant relationships and structures existing at any level of the diversity of life. (E.g. mother > daughter is completely equivalent to bony fish > land animals - they can all be drawn as diamonds and arrows, right?)
  • A strictly phylogenetic classification is formally impossible.
  • Cladism is part of structuralism and therefore characterised by "anti-realism and a metaphysical way of thinking".
  • There exists an objective approach to delimiting paraphyletic groups.
  • It would be preferable to have two parallel classifications, one of clades and one that includes taxa that are allowed to be non-monophyletic.

Is there an objective approach to delimiting paraphyletic groups?

In Aubert's paper, this is apparently dealt with in section 10.7., "Evolutionist Solution". However it remains unclear to me where the actual objectivity comes in. After mentioning that colleagues who promote paraphyletic taxa can use Bayesian phylogenetics, which is true but irrelevant for principles of classification, it continues with "progress has also been made in the field of taxonomy". Three examples are provided:

Monday, January 18, 2016

That editorial in Cladistics

On the weekend, a colleague made me aware of the recent editorial in Cladistics clarifying that all papers in the journal need to use parsimony methods, and she indicated that it had already produced a lot of harsh criticism. Today I read the editorial and several responses including the ones on the Twitter hash tag #parsimonygate. At the moment I am somewhat in two minds about the affair.

To summarise the Cladistics editorial:
  • Authors should always show parsimony trees. Alternative phylogenies can be shown in addition if they are different and there is "a pertinent reason" to do so. This is not really new, as when I published a paper in Cladistics a few years ago I was already asked to do the same. In other journals I have seen the reviewers or editors demand likelihood analyses. I am a methods pragmatist and can live with either. If the data are strong, the results will be the same anyway.
  • The editors consider parsimony analysis to be preferable to other methods for "philosophical" reasons. As far as I can tell, most biologists would be more impressed by biological and pragmatic reasons; I know I am. They also stress repeatability, intelligibility and clarity, implying somewhat that model based methods don't have those. This I find odd except perhaps in the case of certain Bayesian analyses suffering from an over-abundance of unknowable priors.
  • The editors point out that all methods have their weaknesses, and that we have to live with not knowing the truth for certain. Seems obvious.
  • The editors think that they are doing something right because the journal has a high impact factor. Well... let's just say that I have very mixed feelings about impact factors.
To summarise the criticism, let's go through #parsimonygate as of today 10:49 Sydney time:
  • 8x Equating the Cladistics editors to religious fundamentalists or calling them otherwise dogmatic. 
  • 3x Mocking Cladistics as too traditional and/or stuck in the 1980ies. 
  • 1x Some analogy to physics that I don't quite understand. 
  • 3x Ridicule without argument. 
  • 1x Call for boycott. 
  • 1x A different journal advertises itself as accepting all phylogenetic approaches. 
  • 5x Meta, as in expressing amusement at somebody else's comment.
Elsewhere I have seen another call for boycott and somebody mocking the sentence about how we cannot know The Truth with complete certainty, strangely equating this stance with creationism. I think that is exactly backwards, because it is creationists who crave certainty, and it is good scientists who accept that conclusions are tentative and open to future falsification. But okay, it is at least clear the main arguments are that parsimony is outdated and that accepting only papers using a certain approach is dogmatic.

Sunday, January 17, 2016

Types of phylogenetic tree diagrams

This post has two motivations. First, it can serve as a future reference point if I need to mention tree types again, and of course it can be found via search engine by anybody who needs to look this stuff up. The second is my recent observation that some 'evolutionary' systematists have the tendency to call all phylogenetic trees cladograms, perhaps conflating ways of displaying evolutionary relationships with their dubious claim that cladists do not accept the existence of ancestors. I would like to take the opportunity to explain the different ways we can draw trees, what they mean, and what a cladogram really is.

Phylogenetic trees are simple non-cyclical graphs connecting terminals - often species - to show how the terminals are related. In species trees, the internal internodes are common ancestors, and the nodes where branches meet are speciation events. In gene trees, they would be ancestral alleles and mutation events, respectively.

Perhaps the oldest truly phylogenetic tree was drawn by Charles Darwin in his notebook, the famous "I think" diagram. But it was in that case an abstract model to help him visualise for himself common descent, not yet a concrete hypothesis about any specific organisms.


So we have a tree connecting terminals. I will further assume that the tree is outgroup-rooted, so that it has an explicit directionality: In the following examples, the arrow of time points from the left to the right. It could be different. All that follows would work just as well if the trees were turned by 90 degrees and the arrow of time pointed from bottom to top, or if the tree was circular as in the case of Darwin's sketch. What this post is about is simply what the branch lengths on the tree diagram mean, if anything.

Friday, January 15, 2016

Aubert's analysis of phylogenetic terminology, part 6: empirical falsification

Continuing the discussion of this paper from here, here, here, here, and here, and working through the main claims of the paper as I see them:
  • The various definitions provided in the paper are in some way better than the ones that are currently accepted.
  • There is no relevant difference between the systematics-relevant relationships and structures existing at any level of the diversity of life. (E.g. mother > daughter is completely equivalent to bony fish > land animals - they can all be drawn as diamonds and arrows, right?)
  • A strictly phylogenetic classification is formally impossible.
  • Cladism is part of structuralism and therefore characterised by "anti-realism and a metaphysical way of thinking".
  • Cladism is built on biologically unrealistic assumptions that have been empirically falsified.
  • There exists an objective approach to delimiting paraphyletic groups.
  • It would be preferable to have two parallel classifications, one of clades and one that includes taxa that are allowed to be non-monophyletic.

Have the assumptions underlying cladism been empirically falsified?

The abstract of the present paper claimed that the "biologically unrealistic assumptions on which cladism is based ... have been empirically falsified". I was curious what this would be about. As far as I can tell, the only subsection of the paper dealing with the claim is 10.4., Unformitarianism and Punctualism.